The first services from the Book of Common Prayer were conducted in Dakota Territory in 1860 by the Reverend Melancthon Hoyt and the Right Reverend Joseph C. Talbot, Bishop of the Northwest. The following spring, the Rev. Hoyt returned to Yankton, built a log house to accommodate his family and the congregation naming it "St. Johns Church."
The vestry included men prominent in founding Yankton as the territorial capital and organizing the government of Dakota Territory. The House of Representatives of the first territorial legislature met at St. John's in March of 1862. As Yankton grew, the parish grew.
In 1864 it was reorganized and renamed, becoming Christ Church, with a new church building. In 1870 Yankton hosted the first annual convocation of the Episcopal Church in South Dakota. It wasn't long before growth necessitated another move.
The present structure has been in continuous use since November 13, 1882. The altar, baptismal font, pulpit, and rood screen reflect the woodworking talent of men in the parish. The altar hangings and kneelers reflect the nimble fingers of the women in the church. Thus Christ Church is the "Mother Church of the Dakotas".